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Yorodumi- EMDB-34087: The cargo delivery vehicle Hcp-VgrG-PAAR of the Type VI secretion... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34087 | |||||||||
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Title | The cargo delivery vehicle Hcp-VgrG-PAAR of the Type VI secretion system | |||||||||
Map data | ||||||||||
Sample |
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Keywords | T6SS GA3 / cargo delivery system / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacteroides fragilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | He W / Wu K / Zhu L / Wen Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Rep / Year: 2023 Title: Structure and assembly of type VI secretion system cargo delivery vehicle. Authors: Wenbo He / Ke Wu / Zhenlin Ouyang / Yixin Bai / Wen Luo / Di Wu / Hao An / Yucheng Guo / Min Jiao / Qian Qin / Jiaxin Zhang / Yi Wu / Junjun She / Peter M Hwang / Fang Zheng / Li Zhu / Yurong Wen / Abstract: Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS ...Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS delivery tube via its core components: Hcp, VgrG, or PAAR. Here, we report 2.8-Å resolution cryo-EM structure of intact T6SS Hcp5-VgrG-PAAR cargo delivery system and crystal structure of unbound Hcp5 from B. fragilis NCTC 9343. Loading of Hcp5 hexameric ring onto VgrG causes expansion of its inner cavity and external surface, explaining how structural changes could be propagated to regulate co-polymerization and surrounding contractile sheath. High-affinity binding between Hcp and VgrG causes entropically unfavorable structuring of long loops. Furthermore, interactions between VgrG trimer and Hcp hexamer are asymmetric, with three of the six Hcp monomers exhibiting a major loop flip. Our study provides insights into the assembly, loading, and firing of T6SS nanomachine that contributes to bacterial inter-species competition and host interactions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34087.map.gz | 256.9 MB | EMDB map data format | |
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Header (meta data) | emd-34087-v30.xml emd-34087.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34087_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_34087.png | 67.1 KB | ||
Others | emd_34087_half_map_1.map.gz emd_34087_half_map_2.map.gz | 474.6 MB 474.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34087 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34087 | HTTPS FTP |
-Validation report
Summary document | emd_34087_validation.pdf.gz | 995 KB | Display | EMDB validaton report |
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Full document | emd_34087_full_validation.pdf.gz | 994.5 KB | Display | |
Data in XML | emd_34087_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | emd_34087_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34087 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34087 | HTTPS FTP |
-Related structure data
Related structure data | 8graMC 7yw0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34087.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34087_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34087_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hcp-VgrG-PAAR of the Type VI secretion system
Entire | Name: Hcp-VgrG-PAAR of the Type VI secretion system |
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Components |
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-Supramolecule #1: Hcp-VgrG-PAAR of the Type VI secretion system
Supramolecule | Name: Hcp-VgrG-PAAR of the Type VI secretion system / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacteroides fragilis (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.07 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 10 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.4 sec. / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 10500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |